Several lanes were submerged on Kingsway at Glen Waverley, in Melbourne's south-east, after heavy rain in the early afternoon.

Springvale Road was also flooded between the Monash Freeway and High Street Road.

VicRoads has warned motorists to never drive into flood waters.

Thunderstorms this afternoon could see 30 to 60 millimetres of rain fall over Melbourne, Bendigo, Ballarat, Seymour, Wonthaggi and Bacchus Marsh within an hour.

The Bureau of Meteorology said heavy rain, which could cause further flash flooding, was expected to ease later in the afternoon and into the evening.

The city's heaviest rain for the year arrived later on Friday than forecast after the slow-moving cold front sat stationary earlier in the day.

Melbourne was expected to have its wettest day of the year in the 24 hours to 9am, but Bureau of Meteorologist forecaster Richard Carlyon said that could be pushed back a day because the rain was slow moving.

"It's sat almost stationary dumping rain on the western suburbs," the meteorologist said on Friday morning.

Rain soaked the state overnight, with Geelong getting 17 millimetres in the two hours to 8.30am.

Aireys Inlet on the surf coast had 56mm in the 24 hours to 9am, while 59mm fell near Ballarat. Eversley received 53mm and 48mm hit Meredith and Mount Buninyong.

Melton saw 21mm and Avalon was drenched in 19mm.

The bureau had predicted up to 35mm in Melbourne from midnight to 9am, which would have far exceeded the city's highest daily rainfall for this year of 11mm. But by 9am just 7.2mm had fallen.

Road warnings as year's wettest day arrives

"Melbourne will probably get more in the afternoon than we thought," Mr Carlyon said.

"There'll still be some lingering showers for the afternoon commute."

Drivers have been advised to reduce speed, maintain a greater distance between cars, and turn headlights on in reduced visibility.

Meanwhile, strong winds have battered the Port Phillip, Western Port, West Coast, Central Coast and the East Gippsland Coast.

A gale warning is in place for the East Gippsland Coast on Saturday, while strong winds will smack Gippsland Lakes and Central Gippsland Coast.

The SES said it was quiet overnight, with up to 14 jobs in the 12 hours to 7.30am.

A spokesperson said there was "nothing catastrophic at this stage" for rescue crews, who have attended incidents like minor flooding, fallen trees or leaking roofs.

The SES had received 22 calls in 12 hours, most of which came from Dromana on the Mornington Peninsula.

While the bureau says it is not an unusual amount of rain for this time of year, Mr Carlyon said autumn leaves blocking drains could lead to localised flash flooding.

The Mornington Peninsula Freeway was closed between the Nepean Highway in Dromana to Arthurs Seat Road due to minor flooding on Friday morning.

After drought-like conditions, the west gets ready for a deluge

The rain was expected to provide some much-needed follow-up rain for large parts of western Victoria that had suffered through drought-like conditions until a heavy rain band dumped record falls last week.

"A couple of days ago we had that sandstorm [at Mildura] and that's because pretty much the far west of Victoria and eastern South Australia missed out," forecaster Michael Efron said on Thursday.

"It's really important they get this follow-up rain following record dry starts in some parts. Also, a lot of crops have just gone in, so it's important rain."

Graziers have been warned to expect lamb and sheep losses because of cold temperatures and heavy rain and showers in the Mallee, Wimmera, Northern Country, North Central, North East, South West, Central West and South Gippsland.

"There is a risk of losses of lambs and sheep exposed to these conditions," the bureau warned.

The wet, chilly weather was also forecast to bring snow in alpine areas, in altitudes as low as 1000m, with cover of around 5 to 10cm possible.

with Zach Hope and AAP